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X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,G89A Complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AK4 pdb entry 1AK4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.08 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.426 α = 89.99 b = 111.223 β = 101.45 c = 67.78 γ = 89.75
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2001-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.97 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 20 98 0.04 0.04 19 2.05 86252 84527 -3 -3 32.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.93 96 0.251 0.251 2.5 1.95 4202
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1AK4 1.9 19.69 -3 84527 84527 8529 97.58 0.16914 0.16914 0.16204 0.1699 0.23417 0.2394 RANDOM 27.376
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.29 -0.1 -0.46 1.79 -0.18 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.99 r_dihedral_angle_1_deg 5.546 r_scangle_it 4.187 r_mcangle_it 3.799 r_scbond_it 2.788 r_angle_refined_deg 2.589 r_mcbond_it 2.542 r_angle_other_deg 1.059 r_symmetry_hbond_refined 0.253 r_symmetry_vdw_refined 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.99 r_dihedral_angle_1_deg 5.546 r_scangle_it 4.187 r_mcangle_it 3.799 r_scbond_it 2.788 r_angle_refined_deg 2.589 r_mcbond_it 2.542 r_angle_other_deg 1.059 r_symmetry_hbond_refined 0.253 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.234 r_symmetry_vdw_other 0.23 r_xyhbond_nbd_refined 0.212 r_nbd_other 0.21 r_xyhbond_nbd_other 0.165 r_chiral_restr 0.156 r_symmetry_hbond_other 0.059 r_bond_refined_d 0.018 r_nbtor_other 0.018 r_gen_planes_refined 0.014 r_gen_planes_other 0.008 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9408 Nucleic Acid Atoms Solvent Atoms 1123 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling X-PLOR model building REFMAC refinement X-PLOR phasing